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A topological description of hubs in amino Acid interaction networks.

Gaci O - Adv Bioinformatics (2010)

Bottom Line: Once we have compared this type of graphs to the general model of scale-free networks, we analyze the existence of nodes which highly interact, the hubs.We describe these nodes taking into account their position in the primary structure to study their apparition frequency in the folded proteins.Finally, we observe that their interaction level is a consequence of the general rules which govern the folding process.

View Article: PubMed Central - PubMed

Affiliation: Le Havre University, LITIS EA 4108, BP 540, 76058 Le Havre, France.

ABSTRACT
We represent proteins by amino acid interaction networks. This is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. Once we have compared this type of graphs to the general model of scale-free networks, we analyze the existence of nodes which highly interact, the hubs. We describe these nodes taking into account their position in the primary structure to study their apparition frequency in the folded proteins. Finally, we observe that their interaction level is a consequence of the general rules which govern the folding process.

No MeSH data available.


Each time a hub appears in an SSE-IN, we sum its degree according to the amino acid it represents. We repeat the process grouping the SSE-IN by their family and also by their structural class. We normalization to obtain the cumulative connectivity by class. The amino acid Ala acts more often as hub independently of the protein classifications.
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fig5: Each time a hub appears in an SSE-IN, we sum its degree according to the amino acid it represents. We repeat the process grouping the SSE-IN by their family and also by their structural class. We normalization to obtain the cumulative connectivity by class. The amino acid Ala acts more often as hub independently of the protein classifications.

Mentions: For each protein SSE-IN belonging to the same SCOP structural family, we identify the nodes which are hubs; see Figure 4. Then, we group the hubs according to the amino acids they represent and sum their degrees to obtain the amino acid connectivity score by fold families. By repeating this process at the SCOP class level, we calculate and normalize the accumulated connectivity level of amino acids playing the role of hubs; see Figure 5.


A topological description of hubs in amino Acid interaction networks.

Gaci O - Adv Bioinformatics (2010)

Each time a hub appears in an SSE-IN, we sum its degree according to the amino acid it represents. We repeat the process grouping the SSE-IN by their family and also by their structural class. We normalization to obtain the cumulative connectivity by class. The amino acid Ala acts more often as hub independently of the protein classifications.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2877201&req=5

fig5: Each time a hub appears in an SSE-IN, we sum its degree according to the amino acid it represents. We repeat the process grouping the SSE-IN by their family and also by their structural class. We normalization to obtain the cumulative connectivity by class. The amino acid Ala acts more often as hub independently of the protein classifications.
Mentions: For each protein SSE-IN belonging to the same SCOP structural family, we identify the nodes which are hubs; see Figure 4. Then, we group the hubs according to the amino acids they represent and sum their degrees to obtain the amino acid connectivity score by fold families. By repeating this process at the SCOP class level, we calculate and normalize the accumulated connectivity level of amino acids playing the role of hubs; see Figure 5.

Bottom Line: Once we have compared this type of graphs to the general model of scale-free networks, we analyze the existence of nodes which highly interact, the hubs.We describe these nodes taking into account their position in the primary structure to study their apparition frequency in the folded proteins.Finally, we observe that their interaction level is a consequence of the general rules which govern the folding process.

View Article: PubMed Central - PubMed

Affiliation: Le Havre University, LITIS EA 4108, BP 540, 76058 Le Havre, France.

ABSTRACT
We represent proteins by amino acid interaction networks. This is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. Once we have compared this type of graphs to the general model of scale-free networks, we analyze the existence of nodes which highly interact, the hubs. We describe these nodes taking into account their position in the primary structure to study their apparition frequency in the folded proteins. Finally, we observe that their interaction level is a consequence of the general rules which govern the folding process.

No MeSH data available.